Business and Biopdiversity - Ch 2 - Snowball - Pilot 2

Setup

Code

#|
if (!exists("params")){
    params <- rmarkdown::yaml_front_matter('~/Documents_Local/git/IPBES_data_tsu/Assessments/Business/IPBES_BBA_Ch4_Snowball_Pilot_2/snowball.qmd')$params
}

library(bibtex)
library(openalexR)

Thank you for using openalexR!
To acknowledge our work, please cite the package by calling `citation("openalexR")`.
To suppress this message, add `openalexR.message = suppressed` to your .Renviron file.

Code

library(IPBES.R)

library(tibble)
suppressPackageStartupMessages(library(dplyr))

# library(writexl)
# library(ggplot2)
# library(ggraph)
# library(tidygraph)

library(knitr)

x <- list.files(
    "R",
    full.names = TRUE,
    recursive = TRUE
) |>
    sapply(
        FUN <- source
    )


kp <- read.csv(
    file.path("Key Papers", params$key_papers[1]),
    header = TRUE, 
    sep = ",", 
    quote = "\"",
)

Back to Readme

One Generation Snowball

Setup OpenAlex usage and do snowball serarch

Code

#|


fn <- file.path(".", "data", "key_works.rds")
if (file.exists(fn)) {
    key_works <- readRDS(fn)
} else {
    dois <- kp$DOI[kp$DOI != ""] |>
        unique()
    key_works <- oa_fetch(
        entity = "works",
        doi = dois,
        verbose = FALSE
    )
    saveRDS(key_works, fn)
}

ids <- openalexR:::shorten_oaid(key_works$id)

fn <- file.path(".", "data", "snowball.rds")
if (file.exists(fn)) {
    snowball <- readRDS(fn)
} else {
    snowball <- oa_snowball(
        identifier = ids,
        verbose = FALSE
    )
    saveRDS(snowball, fn)
}

flat_snow <- snowball2df(snowball)  |>
 tibble::as_tibble()

Save snowball as Excel file (snowball.xlsx)

Code

fn <- file.path(".", "data", "snowball.xlsx")
if (!file.exists(fn)) {
    to_xlsx(
        snowball = snowball,
        xls_filename = fn
    )
}

To download click here

The column are: (the Concept columns are not that relevant at the moment)

• id: internal id fromOpenAlex
• author: authors of the paper
• publication_year: publication year
• title: title of the paper
• doi: doi of the paper
• no_referenced_works: number of references in the paper which are also in OpenAlex
• cited_global: Number of times the paper has been cited
• cited_global_per_year: standardised number of times cirted (cited_global / number of years published)
• no_connections: number of connections in the rgaph, i.e. either cited or citing a paper in the snowball corpus
• concepts_l0: Concept 0. level assigned by OpenAlex
• concepts_l1: Concept 1. level assigned by OpenAlex
• concepts_l2: Concept 2. level assigned by OpenAlex
• concepts_l3: Concept 3. level assigned by OpenAlex
• concepts_l4: Concept 4. level assigned by OpenAlex
• concepts_l5: Concept 5. level assigned by OpenAlex
• author_institute: Institute of the authors
• institute_country: Country of the institute
• abstract: the abstract of the paper

Citation Network between Works

Code

if (!file.exists(file.path("figures", "snowball_cited_by_count.png"))) {
    plot_snowball(
        snowball,
        name = "snowball"
    )
}

Warning: The shape palette can deal with a maximum of 6 discrete values because more
than 6 becomes difficult to discriminate
ℹ you have requested 7 values. Consider specifying shapes manually if you need
  that many have them.

Warning: Removed 1 rows containing missing values (`geom_point()`).

Warning: The shape palette can deal with a maximum of 6 discrete values because more
than 6 becomes difficult to discriminate
ℹ you have requested 7 values. Consider specifying shapes manually if you need
  that many have them.

Warning: Removed 1 rows containing missing values (`geom_point()`).

Warning: The shape palette can deal with a maximum of 6 discrete values because more
than 6 becomes difficult to discriminate
ℹ you have requested 7 values. Consider specifying shapes manually if you need
  that many have them.

Warning: Removed 1 rows containing missing values (`geom_point()`).

Warning: The shape palette can deal with a maximum of 6 discrete values because more
than 6 becomes difficult to discriminate
ℹ you have requested 7 values. Consider specifying shapes manually if you need
  that many have them.

Warning: Removed 1 rows containing missing values (`geom_point()`).

Fer a pdf of the graph (better resolution) click here

Supplemented Snowball by Edges between all Works

We now supplement the citation network with the citations from the non-key papers, as these are not included in the previous network

Code

fn <- file.path("data", "snowball_supplemented.rds")
if (file.exists(fn)) {
    snowball_supplemented <- readRDS(fn)
} else {
    new_edges <- tibble(
        from = character(0),
        to = character(0)
    )

    works <- snowball$nodes$id

    for (i in 1:nrow(snowball$nodes)) {
        from <- works[[i]]
        to <- gsub("https://openalex.org/", "", snowball$nodes$referenced_works[[i]])
        to_in_works <- to[to %in% works]
        if (length(to_in_works) > 0) {
            new_edges <- add_row(
                new_edges,
                tibble(
                    from = from,
                    to = to_in_works
                )
            )
        }
    }

    snowball_supplemented <- snowball
    snowball_supplemented$edges <- add_row(snowball_supplemented$edges, new_edges) |>
        dplyr::distinct()
    saveRDS(snowball_supplemented, fn)
}

Supplemented Citation Network between Works

Code

if (!file.exists(file.path("figures", "snowball_supplemented_cited_by_count.png"))) {
    IPBES.R::plot_snowball(
        snowball_supplemented, 
        name = "snowball_supplemented", 
        path = "figures"
    )
}

Warning: The shape palette can deal with a maximum of 6 discrete values because more
than 6 becomes difficult to discriminate
ℹ you have requested 7 values. Consider specifying shapes manually if you need
  that many have them.

Warning: Removed 1 rows containing missing values (`geom_point()`).

Warning: The shape palette can deal with a maximum of 6 discrete values because more
than 6 becomes difficult to discriminate
ℹ you have requested 7 values. Consider specifying shapes manually if you need
  that many have them.

Warning: Removed 1 rows containing missing values (`geom_point()`).

Warning: The shape palette can deal with a maximum of 6 discrete values because more
than 6 becomes difficult to discriminate
ℹ you have requested 7 values. Consider specifying shapes manually if you need
  that many have them.

Warning: Removed 1 rows containing missing values (`geom_point()`).

Warning: The shape palette can deal with a maximum of 6 discrete values because more
than 6 becomes difficult to discriminate
ℹ you have requested 7 values. Consider specifying shapes manually if you need
  that many have them.

Warning: Removed 1 rows containing missing values (`geom_point()`).

For a pdf of the reaults (better resolution) click here